Update usage.md

docs/usage.md

@@ -1,13 +1,21 @@
 # DRAM Usage
 
+Here you will find give you basic instructions for running DRAM2
 > _The entire list of pipeline configuration parameters can be found here: [Parameters API](params_doc.md). Here we will give some overviews on how to use important parameters and launch DRAM_
 
-## Introduction
+## Basic command
 
----
+Below is an example of common workflow in DRAM2. The user is calling genes from a directory of MAGs, annotating those genes using all available databases, assessing the qualtiy of each MAG. The user is then summarizing their annotations into user-friendly documents, assigning MAG-level metabolic functions, and generating an interactive heatmap of these functions per MAG. This command in being run from the command line in the background. A more detailed description of flags can be found below
+
+`nextflow run WrightonLabCSU/DRAM --input_fasta [INPUT_FASTA] --outdir [OUTPUT_DIR] --rename --annotate
+--anno_dbs all --qc --summarize --traits --visualize -profile singularity -bg` 
 
 ## Description of command-line options:
 
+```{note}
+All command line options can also be set inside a configuration or params file for set it and forget style parameters instead of needing to be provided each time on the command line. See Nextflow or nf-core documentation for examples.
+```
+
 The general command to run DRAM2 is:
 
 `nextflow run WrightonLabCSU/DRAM [OPTIONS]`
@@ -28,6 +36,29 @@ Because the Nextflow scheduler itself takes of very minimal resources, you do no
 
 If you would like to launch DRAM2 in a slurm job, because Nextflow uses very minimal resources, it is suggested to launch it in a small job, such as 1 CPU and 1 GB of RAM. But this job will need to stay alive for the entire duration of the DRAM2 run.
 
+### Important Command-Line Options Explained
+
+`--input_fasta`
+
+This is the location to the input FASTA files. Can be named as such: `*.f*`. File format can be changed with `--fasta_fmt` argument. See [Parameters API](params_doc.md) for more information.
+
+`--outdir`
+
+This is the desired output directory.
+
+`--input_genes`
+
+If the user has already called genes they may use this option to specify the location of a directory containing `*.faa` files. It is key, and is stated in the GitHub documentation, they these files have headers which are unique to a given sample for correct downstream processes. File format can be changed with `--genes_fmt` argument. See [Parameters API](params_doc.md) for more information.
+
+
+`--annotations`
+
+If the user already has a DRAM2 annotations TSV file, in the correct format, they can provide these using this command-line option.
+
+`--slurm`
+
+This option tells Nextflow to use SLURM as the job scheduler. Additional SLURM options can be specified such as `--partition [PARTITION_NAME]` and `--slurm_node [NODE_NAME]`
+
 ### Important Core Nextflow Options
 
 Nextflow provides many command-line options to control how the pipeline is run. Below are some of the most important ones for DRAM2 users. You will also notice that all Nextflow options can be seen by running:
@@ -54,27 +85,6 @@ If the user has already run this command, or a version of it, Nextflow will look
 
 This option is a Nextflow-provided option which produces a continuously updated log of DRAM2 processes. This is a good place to check how a run is proceeding and is anything has failed.
 
-### Important Command-Line Options Explained
-
-`--input_fasta`
-
-This is the location to the input FASTA files. Can be named as such: `*.f*`.
-
-`--outdir`
-
-This is the desired output directory.
-
-`--input_genes`
-
-If the user has already called genes they may use this option to specify the location of a directory containing `*.faa` files. It is key, and is stated in the GitHub documentation, they these files have headers which are unique to a given sample for correct downstream processes.
-
-`--annotations`
-
-If the user already has a DRAM2 annotations TSV file, in the correct format, they can provide these using this command-line option.
-
-`--slurm`
-
-This option tells Nextflow to use SLURM as the job scheduler. Additional SLURM options can be specified such as `--partition [PARTITION_NAME]` and `--slurm_node [NODE_NAME]`
 
 #### Pipeline Steps